I put my os and core programs -- everything I need to be productive -- on one partition, my documents on a 2nd, and games and media on a 3rd. after I have the system working as I want, I image the os partition so any time I need to I can wipe windows and reimage it. the os partition is the one most likely to get hit/ruined by virus. I also like to just reinstall windows once in a while to clean out the crud.
this makes backup easier too.